Implement CLI command atomcommit plan to analyze git working tree and produce atomic commit plan

[rogerchappel]

Summary

This PR hardens the existing atomcommit plan CLI command with comprehensive tests, fixture repos, and documentation. The core functionality was already implemented in f90d5ba (Add deterministic plan command). This PR focuses on verification, determinism, and reviewable documentation.

Changes

1. Fixture Repositories

• Added fixtures/setup-mixed-changes.sh — script to create deterministic test repos
• Added fixtures/mixed-changes-repo — generated fixture with 9 file changes across 4 groups:
  • Modified source files
  • New and modified test files
  • Documentation changes
  • CI/CD configuration changes
  • Renamed files
  • Deleted binary files
• Added .gitignore to exclude generated fixture repos

2. Test Suite Enhancements (6 tests total)

Existing tests (3):

• ✅ Parses git name-status metadata including renames
• ✅ Builds deterministic grouped plan and markdown
• ✅ CLI reads local git diff without mutating the working tree

New tests (3):

• ✅ Fixture repo validation — verifies CLI against repo with mixed changes, checks all groups and risk flags
• ✅ Commit message validation — asserts suggested messages are meaningful and follow conventions
• ✅ Snapshot test — verifies exact structure, file counts, and risk flags match expected output

All tests pass and output is deterministic across multiple runs.

3. Documentation

README.md:

• Added overview section with key features
• Full usage examples with sample output
• Grouping logic table (documenting how files are classified)
• Risk flag definitions and trigger conditions
• Fixture repository documentation

docs/README.md:

• Added decision log documenting grouping logic rationale
• Risk flag trigger conditions and review rationale
• Future enhancement ideas

4. Package Configuration

• Updated package.json test script to only run test/**/*.test.js (exclude fixtures from test runner)

Verification

Test Results

✔ parses git name-status metadata including renames
✔ builds deterministic grouped plan and markdown
✔ cli reads local git diff without mutating the working tree
✔ fixture repo with mixed changes produces expected plan
✔ suggests commit messages based on grouped files
✔ snapshot: mixed changes produce consistent plan

6 tests, 6 pass, 0 fail

npm test
bash scripts/validate.sh

Both pass all checks.

Manual Testing

# Test against fixture repo
cd fixtures/mixed-changes-repo
../../src/index.js          # Markdown output
../../src/index.js --json   # JSON output

# Test determinism (run twice, compare)
../../src/index.js > /tmp/run1.md
../../src/index.js > /tmp/run2.md
diff /tmp/run1.md /tmp/run2.md   # No differences

Design Decisions

Grouping Logic

Files are grouped based on path and extension:

Group	Pattern
CI and repository automation	.github/*
Documentation	docs/*, *.md files
Tests	test/*, *.test.js
Source code	src/*, *.js source files
Root files	Top-level files not matching above

Rationale: Co-locates related changes for focused review (docs together, tests together, etc.).

Risk Flags

Flag	Trigger
deletion	Git status D (file deleted)
rename	Git status R (file renamed/moved)
binary-file	No text stats available
large-change	Additions + deletions ≥ 400 lines

Rationale: Flags highlight changes requiring extra review attention.

Commits

1. test: add fixture repo for mixed changes with snapshot test
2. test: add snapshot and fixture tests for deterministic plan output
3. docs: expand README with usage examples, grouping logic, and risk flags

All commits are focused and atomic.

Human Review Needed

• ✅ Approve grouping logic and risk flag criteria (documented in README and docs/README.md)
• ✅ Validate commit message suggestion quality (documented in README examples)

Links

• Issue: N/A (implementing task brief)
• Branch: agent/implement-cli-command-atomcommit-plan-to-analyze-git-working-tree-and-pr